The Village Hidden in the Fog
by Uzumaki D. Jiro
Summary: Yahiko, Nagato, and Konan find a bloody and beaten Naruto during a mission in the Hidden Leaf and end up adopting him. He comes back 7 years later during the Chunin Exams to make himself known. Watch as Naruto becomes the Hero of the Shinobi Nations. AU, Strong and Smart Naruto, [Naruto x Fu].


"Normal Speech"

'Quotes'

' _Thoughts'_

" **Biju/Summoning"**

' _ **Biju/Summon thoughts'**_

 _Letters/Reports/Other Documents_

 **A/N: Hello everyone, my name is Jiro Uzumaki. This is my first attempt at writing a fanfiction, so please bear with me. Reviews and criticism are welcome, and if I made any errors then don't hesitate to point them out, or if you have a general question contact me via PM or review.**

 **This story was inspired by "Naruto: Stitch Demon" by SilentFang. Yahiko, Nagato, and Konan all found a new hidden village together and go to the Hidden Leaf for an alliance. However, they make an unexpected discovery. Some members of Akatsuki are still allied with them, but others are evil and will still pose a threat. I have used existing characters in the Naruto-verse, but have changed their stories a bit. I do not have any OC's, yet, but might include them as very minor characters.**

 **Thanks for reading, be sure to review, and enjoy!**

 **I do not own Naruto. All rights of ownership are reserved by Masashi Kishimoto.**

* * *

 **Chapter 1: New Family**

Run. That's all he could do. Run as fast as could and find a place to hide so they wouldn't catch him.

A small child, no more than six years old was pushing his small body to its limit. His sun-kissed blonde hair matted with blood and dirt, his slightly tanned skin covered in cuts and bruises, his cut up beige shorts and the remains of his black shirt, torn and bloodied. The ruined garments were all that was left of his worldly possessions, not that he had much in the first place, but since he was kicked out of the orphanage, he can really say he had nothing. When the matron of the orphanage kicked him out she yelled at him 'to never come back, you filthy demon.' He wandered the streets for hours and later encountered a mob that formed to kill him. They planned on 'sending the demon back to hell' as they proclaimed, but he was able to escape while they were distracted by their excitement for his death.

Pushing through his pain, he kept running towards a large tower in the center of the village, the one place he could go to seek help, but he was still quite far away. In an effort to throw off his pursuers, he turned down a narrow side street, then another, and another, until finally coming to a stop in an alleyway when he was sure he had lost them. Panting, he looked for somewhere to hide from the mob until he was rested and sure it was safe enough to start making his way towards the tower again. He would be safe once he was there. The Old Man would protect him, just like he always did. He was about to hide behind some old trash cans and garbage bags when he heard something.

Looking up he saw a man crouched on a roof, looking dead at him with a malicious smile on his face. "I FOUND HIM! THE DEMON IS OVER HERE!"

' _Oh no. No, no, no, no, NO! THERE WERE NINJA IN THE MOB!'_ He thought frantically. He was still too far from the tower! There was no way he could escape now! Not if there were ninja after him as well as the normal villagers! Just as he was about to run again, two more men appeared and cut off his escape route. They slowly started to advance, forcing the boy to back into a wall. As he fell to the ground on his butt, shivering in fear, the rest of the mob caught up. They were all shouting the same thing:

"TIME TO DIE, YOU DEMON!"

"YOU'LL PAY FOR WHAT YOU DID!"

"HOW DARE YOU CONTINUE TO SHOW YOUR FACE AROUND HERE?!"

"WE WILL FINISH WHAT THE YONDAIME STARTED!"

It was always like this. The entire village absolutely hated him, and he didn't know why. He had never done anything to them, yet they still hated at him. They still beat him. They still gave him rotten food to eat and abused him for no reason on an almost daily basis. It was maddening. Especially when nobody would tell him the reason. Whenever he asked, the beatings just seemed to get worse.

' _Why? Why does this always happen to me?' '_ The boy thought to himself _'Am I really a demon? Did I really do something so awful to these people that they feel the need to beat me?'_ He was forcefully brought out of his thoughts by a bone shaking kick to his face. Cheers echoed throughout the crowd and more people started to join in, punching, kicking, even stabbing and slashing at him. All he could do was roll himself up into a ball and cry as he took their blows all over his body.

It went on for what seemed like forever, until, suddenly, his tormentors stopped. The blonde boy looked up and saw the crowd begin to part, and a man with silver hair with a bandana headband on top, navy blue pants, and a navy blue long sleeved shirt under a green flak jacket walked up to him. He was obviously a shinobi, at least Chunin rank if the flak jacket was any indication.

"Hold the demon down." the silver haired man said while pulling a sharp object out of a pouch on his left leg. "I want to finish this once and for all." Four men walked over to the beaten child and kicked him over so he was lying flat on his stomach. They, then, proceeded to rip off the remains of his shirt as they held down his arms and legs. The man in the flak jacket bent down and looked the child in his eyes, taking satisfaction in the fear they displayed.

"Well now, little Demon" the man said in a mocking tone. "It wasn't nice of you to run away from us in the middle of our fun! I thought you liked death and destruction seeing as how you almost destroyed the entire village at one point!"

"What are you talking about?!" the child screamed. "I never did that! Please let me go!" he pleaded as his tears started to mix with the blood and grime on his face.

"QUIT LYING YOU DEMON SCUM!" The man yelled as he kicked him in the side, eliciting a yell from the captive boy. "Now stay still and let me continue marking you, so the world will know exactly what you are, before we send you back to hell!" the silver haired man yelled out so the mob could hear him clearly, eliciting another round of cheers. With that said, he plunged his weapon into the child's back until he could hear the dull _THOK_ of his kunai hitting the back of the boy's rib cage, and started cutting.

The child screamed as loud as he could, desperately crying out for help from someone, anyone, to help him. As his eyes darted around searching for a way to escape, all he could see was the looks of glee and satisfaction on the crowd's face, before his vision started to go black. In the back of his mind, he almost hoped that he would never wake up again.

* * *

Three figures stopped at the North gate of the Hidden Leaf Village. Each were wearing a black cloak with a red cloud pattern adorned on it, the mark of their organization.

The first was a man that had lightly tanned skin, vibrant, spiky orange hair, and light blue eyes that exuded mischievousness and leadership. To his left, a man slightly taller than him with very pale skin and dark red hair (almost the color of blood), with very dark goggles covering his eyes, gazed upon the enormous gate. He seemed to have an air of slight nervousness around him, which was quite unusual for him. The third member, a female with pale blue hair, adorned in a bun held up by an origami flower, and amber eyes with a piercing on her lower lip. She seemed to have a calmness and serenity around her.

"Well guys," the leader exclaimed with a big smile "it looks like we finally made it to the Hidden Leaf! And one step closer to our dream... I hope." He looked to the man next to him. "Yo, Nagato. You sure you're going to be okay?" he asked, turning to the now identified Nagato. "Even though this is sensei's home village, your parents' murderers are from here too."

"Yes, Yahiko." Nagato replied. "I will be fine. Jiraiya-sensei has helped me let go of my hatred a long time ago. I will not hate this village for the actions of the few." Yahiko just nodded then turned to their female companion, as she hooked her arm around his. "Ready to go Konan-chan?" Yahiko asked the blue haired beauty. Konan nodded and gave him a small, reserved smile and the three walked into the village.

As they made their way down the main road, they stopped and noticed there was some sort of celebration going on. There were food stalls and games all along the street. "Oh right! It's October 10th right?" Yahiko asked. "This must be the festival they throw every year to honor of the defeat of the Kyubi six years ago by the hands of the Fourth Hokage." Konan said while observing everything. Civilians and ninja alike were walking around enjoying the festivities; children were running around laughing and having a good time. The trio slightly smiled as they took in the lighthearted atmosphere and continued on their way towards the Hokage tower, where the leader of the village worked.

After walking a few blocks down the road, Nagato stopped, suddenly, and turned his head, staring intently down a darkened side street with a puzzled expression. Noticing their companion was no longer with them, Yahiko and Konan stopped and looked back at him.

"Hey man, is everything alright?" Nagato was quiet for a moment before answering. "I feel... an unusual amount of chakra over there. I'm going to go look. Follow me." He took off down the side street while his companions just looked at each other and followed behind him.

"What is so unusual about this chakra signature that you're making us go out of our way to see? We _are_ in a ninja village. There are bound to be a few strange chakra signatures every now and then." Konan asked while looking at Nagato. He was quiet for a moment and then shook his head. "It's not just strange. It's just how much of it there is. Or more importantly, how much of it there _isn't_. At first I thought it was just an animal or something, but... it feels too human-like. The thing that's worrying me is how weak the signal is, and the fact that it's not moving. Whoever it is needs help, and fast."

Just as Nagato finished, the trio came upon a small street cluttered with trash and drops of a red liquid everywhere. Upon closer inspection, they found it to be blood. "Oh no" Nagato whispered before turning to a space between two buildings. There, lying in the middle was a small boy, bruised and bleeding profusely from his back and a broken arm that was bent horribly out of place.

"Oh my god!" Konan yelled.

"Nagato, go find the Hokage and tell him about this, NOW!" Yahiko barked out at his friend.

"Roger!" Nagato took off at full speed, jumping to the rooftops and heading toward the Hokage tower. Yahiko and Konan ran up to the boy, who was apparently conscious, but couldn't move too well. Upon hearing Yahiko's yell, the boy's eyes widened and he immediately tried crawling away, but could only make it a few inches before he collapsed again.

"P-Please," the boy said before trying to inch his way in the opposite direction from them again. "Pl-please, no more! I don't want to die! I'm sorry for whatever I did! Just please, don't hurt me anymore!" The boy was crying, tears falling out of his deep cerulean eyes and smudging the dirt and blood caked on to his face.

Upon seeing this, Yahiko immediately stopped his advance. "It is alright little one." He said in a low voice. "We are here to help-"

"LIAR!" the boy yelled back, his voice angry and hoarse and filled fear. "I WON'T FALL FOR THAT AGAIN! THE LAST TIME SOMEONE SAID THAT THEY TRIED TO BURY ME ALIVE!" He somehow managed to make it to the other side of the alley. His back was against the wall and his good arm clutching his broken one. Konan walked forward a few steps and kneeled down in front of him, and held out her hand, mentally frowning at the fact that the boy seemed to flinch when she did so.

"It's okay young one." she said in the kindest way possible. "We won't hurt you. We just want to get you to a hospital and fix you up. Don't worry, you'll be fine in a little while-"

"STOP LYING!" the boy yelled again causing Konan to frown.

 _'Whoever did this to him had obviously done it multiple times before. He won't trust anyone.'_ she thought sadly.

"She isn't lying," said a voice from behind them. The three in the alleyway turned to see a man in his late fifties wearing white and red robes and a matching hat with the kanji for 'Fire' on it, with Nagato standing beside him. He was Hiruzen Sarutobi, the reinstated Third Hokage. "It is okay Naruto. They are friends. Let's go to the hospital and get you fixed up." The boy, now identified as Naruto, processed what was said to him before, finally, nodding and, hesitantly, reached out for Konan's hand. As he took it, she lifted him up as best as she could, without agitating his injuries, and handed him to the Hokage who muttered a quick thanks.

The adults noted that his injuries were far worse than they thought. While the wounds on Naruto's arms and legs were mostly superficial and would heal relatively quickly, the wounds on his torso were deep. He has cuts and lacerations all over his stomach and chest, a large bruise directly over his navel, and many small burn marks all over his sides. The Hokage gave a solemn look to the boy as he passed out from the pain of his injuries, before turning towards the hospital with the other three trailing behind him.

* * *

A few hours later, Yahiko, Nagato, Konan, and Hiruzen were sitting in a hospital room with a bandaged and sleeping Naruto on the bed. "Lord Hokage..." Yahiko said while looking at the boy. "Why did this happen? Who would ever stoop so low as to beat a small child and leave him for dead?" Yahiko was furious, but holding himself back. Konan was also trembling, clenching her fists repeatedly, and Nagato held a scowl on his face. The Hokage sighed and looked at the three of them, before doing a few quick hand seals and setting up a basic privacy barrier so no sound could get in or out.

Sighing again, Sarutobi replied "I suppose I at least owe you three an explanation as gratitude for finding him before he was hurt more, or worse. You have heard of the Kyubi attack on this village six years ago, correct?" After a slight pause all three of them nodded and the hokage continued "During that battle, Minato Namikaze, our Fourth Hokage defeated it at the cost of his own life..."

"Wait a minute. I thought Biju couldn't be killed?" Yahiko said while scratching his chin.

"They can't." A new voice appeared from the window, and when everyone looked over they saw a very big man with long spiky white hair in a ponytail, wearing a pale green outfit with a red vest over it and a horned headband with the kanji for "Oil" on it.

"Jiraiya!" the Hokage exclaimed, a bit surprised to see his old student "Hello sensei." Jiraiya said back absentmindedly while walking over to the hospital bed, inspecting the still sleeping Naruto, then turning to the other occupants of the room.

"How did you get in here sensei? I thought there was a privacy barrier up." Nagato asked.

"Oh please. Just who the hell do you think I am? I am the mighty Toad Sage of Mt. Myouboku! Do you honestly think a tiny privacy seal will keep me out of any place I really wanted to go? he replied. Nagato just nodded and Konan spoke up.

"Getting back on track, if Biju cannot be killed then how did the Fourth Hokage stop the Kyubi?"

"Well," the Hokage started, grateful to get back to his explanation, before Jiraiya brought them too off topic. "Biju are large masses of malevolent chakra given a form, so in a sense they aren't _really_ alive. The only way to stop a Biju is to seal. Whether it be in a very old, very powerful artifact. Or…"

"Inside a newborn child." Jiraiya finished as the Hokage nodded slowly.

"Then he is…" Konan started as her and her two companions eyes widened

"Yes." Hiruzen replied "He is the container of the Nine – Tailed Fox, strongest of the nine Biju." The Hokage sighed before continuing "Somehow, this information had leaked to the general public despite my best efforts. Lord Fourth wanted this child to be seen as a hero. As the person who constantly holds back the Kyubi from destroying everything and killing everyone in this village. But the people didn't listen. All they see him as is the raging monster who attacked the village and slaughtered their loved ones."

"So…" Nagato spoke up "They see him has the proverbial kunai, and not the pouch that said kunai is stored in?" Jiraiya and Hiruzen both nodded solemnly "Idiots! They permanently scarred a small child's mind and body and forever engraved his back with a derogatory term, because they choose not to understand something that was explained to them?!" Hiruzen and Jiraiya nodded again, knowing that the scar he was referring to was the word 'DEMON' that was cut into Naruto's back. The Kyubi's healing abilities should be able to heal the rest of the scars and burns he received today that couldn't be fully healed by medical ninjutsu.

"What of the boy's parents?" Konan asked. "I would hate to think they abandoned him just because of what he hold."

"They both died in the attack." Jiraiya answered her. Everyone went quiet, the only sound in the room coming being the rhythmic beeping of Naruto's heart monitor.

"Well…" Yahiko started "Why not put the kid up for adoption? I'm sure there has to be at least _one_ person out there who would take him in." Sarutobi shook his head slowly. "I tried that. No civilian families would take him in, and we cannot give him to one of our ninja clans seeing as they would only take advantage of his- or rather, his 'tenants' power for political gain." The room quieted down once again until Nagato looked at Jiraiya and spoke up.

"Sensei. Isn't Naruto the name of the character in your first book? Does that mean you are related to him somehow? I doubt you came to see him just because of his 'tenant'."

Jiraiya was silent for a moment before answering. "Yeah… I'm the kid's godfather. His parents did indeed name him after the character in my book."

"So why not adopt him and take him with you?"

Jiraiya looked at his three students before saying "I couldn't. I'm constantly on the road maintaining my spy network. It would be too dangerous for me to take a kid with me. Besides, I didn't even know he was being treated like this. This is my first time being back in the Hidden Leaf for four years… I thought he was still in the orphanage or already adopted or something… I knew he wouldn't be treated fair, but I didn't think it would ever get this bad."

The Hokage nodded "Seeing as how I am almost constantly busy, I cannot take him in either. I don't know what else to do-"

"I'll adopt him." Nagato blurted out, much to the surprise of Hiruzen and Jiraiya.

"But Nagato, aren't you three travelling as well? That's just putting him in the same situation as he would be in if I took him." Jiraiya stated.

"Yes we are travelling," Yahiko spoke up "But it's nowhere near as dangerous as what you're doing sensei." The hokage raised an eyebrow.

"Now that you mention it Yahiko-san, what exactly _are_ you travelling for my boy?" the Hokage asked. "If I recall you had requested a meeting with me until Nagato-san came and brought me to the alley."

Yahiko nodded before answering "Nagato, Konan, and I are trying to build our own hidden village. The Village Hidden in the Fog."

This piqued Sarutobi's interest. _'They are obviously good people with a good dream, but I am a bit uneasy about letting almost total strangers take Naruto away. And I'm sure the Council won't like that I'm giving them our Jinchuriki, but…'_ Hiruzen gave Naruto a quick glance _'I at least owe him this much. I have failed not only him, but both Minato and Kushina for allowing this to happen without my knowledge.'_

Stroking his beard, Sarutobi addressed Yahiko "So I'm assuming you came to me to sign a document saying that I, along with the rest of the Hidden Leaf and its council acknowledge you as an independent nation?"

Yahiko nodded. "As you know, a country cannot have its own hidden village until a majority of the five Kage from the largest villages agree. We are travelling to each of the five major villages to try and get recognized."

Hiruzen nodded. "Can you tell me a bit about your village Yahiko-san?"

"Of course, Hokage-sama. We are located in the Land of Swamps, and have already received the Daimyo's support and permission to build our village there. We, also, have our own military force, both a shinobi and civilian academy built, and are working on a system to stabilize our economy. We have, also, recruited missing-nin, runaways, orphans, refugees, and 'undesirables', because we want our village to be a safe haven for others. Along with your signature of approval, we were also hoping for some sort of treaty or trade agreement with you."

"I see. Impressive." Hiruzen said as he was contemplating everything Yahiko told him. "But before I can sign this I must know that your country is trustworthy. I know you three personally are very noble, if you weren't, you wouldn't have saved Naruto here." He said motioning to the blonde boy "And the fact that you are Jiraiya's old students is nothing to sneeze at either, but I need to see some sort of proof that your village won't hinder or betray mine."

"Konan." Yahiko said looking to his female companion. Konan nodded and withdrew a blue scroll with a wave pattern on it from her cloak and handed it to Yahiko. "This is our letter of acknowledgement from the Fifth Mizukage, Mei Terumi." He said "It, also, includes our trade agreements and a possible alliance if we are successful and help stabilize their economy as well, since they are still recovering from their civil war. She, also asked us to take in refugees from the civil war and bloodline purge because there is still tension and animosity within the Land of Water."

Sarutobi just took the scroll, reading it over quickly and handing it back to Yahiko while nodding. "Very well, while we cannot have an alliance yet, I will allow trade and acknowledge you as a full-fledged hidden village. May I ask what other Kage you have spoken to thus far?"

Yahiko nodded before answering "Including you, there is the Mizukage, who accepted us, and the Tsuchikage who denied us." _'No surprise there.'_ Hiruzen thought. _'Onoki was always an isolationist and hated the idea of minor villages,'_

Thinking for a bit longer Hiruzen nodded and came to a decision. "Very well. I will allow you to adopt Naruto.' Upon hearing this, the three fog-nin and Jiraiya all lit up 'I will start drawing up the adoption papers as soon as he is awake. Oh, speak of the devil…'

Everyone turned to see Naruto waking up. He looked around at everyone in the room before his eyes rested on the Hokage. "Jiji… where am I? What happened?" The hokage gave Naruto a small smile an answered "These three nice people found you half dead in the streets and helped bring you to the hospital." Naruto looked at the Fog group and muttered a barely audible 'thank you.' "That's not all Naruto." Hiruzen said as the boy turned back to him. "They also wish to adopt you. You can have a real family if you wish."

At this, Naruto's eyes widened to the size of saucers. _'A… A family? I thought I wasn't allowed to have a family? I thought nobody wanted me?"_

Nagato, seeing the look on Naruto's face, smiled a bit before walking over and sitting in an empty chair next to his bed. _"_ Hello Naruto." He said in a soft voice. "My name is Nagato." He offered him a small smile.

' _Wow'_ Naruto thought. _'He has cool hair. And he seems really nice...'_

"I'm going to be your new father."

Naruto looked at him for a second and said "Otou-san?" Nagato nodded and hugged him close. He tensed a bit, causing him to frown slightly, but he soon melted into the embrace. It was the nicest and gentlest thing he had ever experienced. Behind him, Yahiko and Konan decided to introduce themselves as well.

"Hey kid, My Name is Yahiko! Well, I guess if Nagato is your father, then that makes me you're your uncle and Konan your aunt." Yahiko blurted out with a huge grin on his face. Naruto looked over at Yahiko and Konan and smiled. "Oji-san…Oba-chan" he said in a small voice.

"That's right!" the orange haired man responded before walking over and ruffling Naruto's hair while laughing

Naruto nodded at him then took another look at his new family before he started crying.

Nagato chuckled softly as he hugged him again and asked "Come now, why are you crying?"

Naruto just looked at him and said "I-I was always told that I w-wasn't allowed to have a family… that I didn't deserve one because I was a demon…"

"NARUTO!" Hiruzen shouted causing the blonde to jump a bit. "You are not and never will be a demon. Don't let _anyone_ tell you otherwise, okay?" The small boy just nodded and cried more.

"Isn't this great sensei!" Yahiko turned around to see Jiraiya no longer there. He wondered when he left before shrugging and turned back to the newest addition to his family who was still crying tears of joy into Nagato's cloak.

* * *

One month later, Naruto was fully healed, was bought new clothes, and after a LOT of covering up so the Hidden Leaf's Civilian and Shinobi council would think he died from his last beating (something the civilians and most shinobi were ecstatic about and most with the exception of two or three Clan heads, two civilians, two ANBU officers, and some Jonin and Chunin who were told later), Yahiko, Nagato, Konan, and Naruto were ready to leave Konoha.

A small group of spectators were just outside the main gate, watching as the family made their way down the main road with Yahiko holding an excited Naruto on his shoulders, towards their next destination, the Hidden Sand Village. Hiruzen was standing at the gate, along with Teuchi Ichiraku and his daughter, Ayame, the only people that let Naruto eat food at their small ramen stand (and would have adopted him themselves if they weren't so poor) smiling sadly. Although Hiruzen never had much time to spend with Naruto, the small energetic was like a grandson to him. It was hard watching him go, but after seeing him hurt so badly and how he was so happy to finally have a real family, Hiruzen knew it a good decision.

Right before they were out of eyesight, the Hokage noticed the group stop, Naruto flailing his arms and climbing off of Nagato's shoulders before running back up to the old Hokage and the Ichiraku family. "Jiji! Teuchi-Ojisan! Ayame-Neesan!" Naruto deeply bowed before saying "Thanks for everything! I promise I'll be back to visit soon!" before gathering them in a group hug and without waiting for a reply, ran back to his new family that was waiting for him with smiles on their faces. Hiruzen smiled proudly as Teuchi yelled that he would always have a seat at their restaurant and Ayame yelled to be safe.

"Hey, Naru-chan?" Konan asked as Naruto was getting back on Nagato's shoulders.

"Hmm?" Naruto replied while looking at his aunt.

"What was so important that you had to run all the way back to the gate to tell them?" Naruto just grinned widely and said "I made a promise! A really important one, too."

"Oh really?" Yahiko said looking at his adoptive nephew. "Promises are a big responsibility! Be sure not to break it."

Naruto just laughed and said "Of course not! I never go back on my word, Oji-san!"

Yahiko chuckled slightly as they continued to make their way down the road.

* * *

 **A/N: Well, that's the first chapter. I hope you all like the where the story is going.**

 **Seeing as how this is the first chapter, it is like the prologue. The next chapter makes a huge time skip, about a week and a half before the beginning of the Chunin exams. It's there where we'll meet Naruto's team and friends and see how he grew up in Fog. Important things that happen between him leaving with his new family and the start of the next chapter will be covered in flashbacks. Thanks for reading, see you next chapter! And don't forget to review!**


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